How RnBeads define promoters?

Hi there, How R package {RnBeads} define promoters? Like two promoters annotation derived from RnBeads as following:

               Chromosome Start   End Strand   symbol   entrezID CpG           GC   C   G
  ENSG00000223972  chr1  10369 12368    +      DDX11L1    100287102;100287596 140 1208 587 621
  ENSG00000227232  chr1   29307 31306   -       WASH7P    653635;100287171    78 1047 580 467

It seems promoters annotation in RnBeads is + or - 1000bp from TSS, but if I need to customize promoters from + or - 2000bp from TSS, how to make it happen in RnBeads?

Thanks for anyone who can give me a hint :)

rnbeads promoters tss

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updated 8.5 years ago by Santosh Anand

• written 8.7 years ago by sugus

1 answer

Promoters are defined as the regions 1.5 kb upstream and 0.5 kb downstream of the transcription start sites. Custom annotations can be included using the function rnb.set.annotation().

Check the section 5.2 and 5.2.1 of the manual.

http://www.bioconductor.org/packages/3.7/bioc/vignettes/RnBeads/inst/doc/RnBeads_Annotations.pdf

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written 8.5 years ago by Santosh Anand